I keep getting error messages when submitting HTSeq jobs, using both -
(a) sorted (by chromosomal coordinates) and
(b) unsorted bam files
I made sure to specify the appropriate order in the HTSeq options: -r pos for both sorted and unsorted. I'm re-running samtools now to sort by name, but I'm not sure that's necessary (since you can specify position in the order option.)
Here is the error message I get when specifiying the unsorted bam file:
Error occured when processing SAM input (record #1794713 in file /xx/xx_Aligned.out.bam
I am not sure why it's referring to a sam input. Am I better off converting to sam? Is there anything else I could be missing
And here is the error message I get when specifying the sorted bam file:
Error occured when processing GFF file (line 1611183 of file /xx/GTF/Homo_sapiens.GRCh37.65.gtf)
I'm sure this is a common problem and that there are many posts about this. I am certainly looking into it but in the meantime was hoping to get any feedback if you're familiar with this. Clearly I'm a newbie to this kind of analysis.
Thank you so much!
1 answer
Try to upgrade the library "pysam", it could be a fast solution.
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Was that the GTF file that you aligned against? How did you do the alignment?
Andrew,
Thanks for the quick response. Yes. I used both an existing (previously used for cuffdiff analysis and that worked well) and a newly-downloaded GTF file. For the alignment, I used STAR with unsorted bam output and then used samtools to create the sorted bam files (by position).
Can you amend your post with the commands you've ran?
Since I sorted by chromosomal coordinates, I thought specifying
-r poswould be sufficient. Not sure why I would get the GTF processing error though (and I'm using the same gtf file as before). I will try to re-sort by name and use the-r nameoption to see if that magically helps resolve this.Did you run the command with
-f bam? Because sam is the default type.Hi! Yes I did. I added the options I used above.